RNA-Seq sequencing depth information from NCBI

[alittleboy]

I am working on several datasets downloaded from NCBI SRA. For example, the zebrafish dataset accessible from:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44233

is used for my analysis. However, I am not sure how can I obtain the sequencing depth of this experiment from some meta-data (say, the SraRunInfo.csv file). I summarized the data into a read count matrix, and calculate column sums:

Gata4.1 Gata4.2 Gata4.3 WT.1 WT.2 WT.3
16779626 37906530 12574486 19009161 21119399 15302189

It seems that different samples have different sequencing depths... is that correct? So, what is (are) the sequencing depth(s) for this experiment?

Thanks!

[GenoMax]

If you want to estimate the sequencing depth at each base precisely then you will need to do some alignments and calculate the coverage based on the reads that cover each base.

If you just divide the amount of sequence in each sample file (bp's) by the genome size then you have a theoretical gross estimate.

It is impossible to generate exactly the same amount of sequence data for each sample (unless you artificially do so programmatic sub-sampling). Normally each sample will have differing number of reads/data.